Add writing capabilities for freesurfer triangle files

Produces files identical to freesurfer up to the point that nibabel
reads. There is additional information after a freesurfer generated
file, but nibabel reads equivalent data and PySurfer displays these
files fine.

Author: effigies

nibabel/freesurfer/io.py

@@ -92,6 +92,32 @@ def read_geometry(filepath):
     coords = coords.astype(np.float)  # XXX: due to mayavi bug on mac 32bits
     return coords, faces
 
+def write_geometry(filepath, create_stamp, coords, faces):
+    """Write a triangular format Freesurfer surface mesh.
+
+    Parameters
+    ----------
+    filepath : str
+        Path to surface file
+    create_stamp : str
+        User/time stamp
+    coords : numpy array
+        nvtx x 3 array of vertex (x, y, z) coordinates
+    faces : numpy array
+        nfaces x 3 array of defining mesh triangles
+    """
+    magic_bytes = np.array([255,255,254],dtype=np.uint8)
+    with open(filepath, 'wb') as fobj:
+        magic_bytes.tofile(fobj)
+        fobj.write("%s\n\n" % create_stamp)
+
+        # On a Linux box, numpy uses opposite byte order to freesurfer
+        np.int32(coords.shape[0]).byteswap().tofile(fobj)
+        np.int32(faces.shape[0]).byteswap().tofile(fobj)
+
+        # Coerce types, just to be safe
+        coords.astype('>f4').reshape(-1).tofile(fobj)
+        faces.astype('>i4').reshape(-1).tofile(fobj)
 
 def read_morph_data(filepath):
     """Read a Freesurfer morphometry data file.

nibabel/freesurfer/tests/test_io.py

@@ -1,11 +1,12 @@
 import os
 from os.path import join as pjoin
+import time
 
 from nose.tools import assert_true
 import numpy as np
 from numpy.testing import assert_equal
 
-from .. import read_geometry, read_morph_data, read_annot, read_label
+from .. import read_geometry, read_morph_data, read_annot, read_label, write_geometry
 
 
 have_freesurfer = True
@@ -36,6 +37,19 @@ def test_geometry():
     assert_equal(0, faces.min())
     assert_equal(coords.shape[0], faces.max() + 1)
 
+    # Test equivalence of freesurfer- and nibabel-generated triangular files
+    # with respect to read_geometry()
+    surf_path = os.tmpnam()
+    create_stamp = "created by %s on %s" % (os.getlogin(), time.ctime())
+    write_geometry(surf_path, create_stamp, coords, faces)
+
+    coords2, faces2 = read_geometry(surf_path)
+
+    # Remove 
+    os.unlink(surf_path)
+
+    assert_equal(coords, coords2)
+    assert_equal(faces, faces2)
 
 @freesurfer_test
 def test_morph_data():